Thursday, 1 October 2020

Day 199 of self-isolation - Herd immunity

Herd immunity

What is herd immunity, and what do the numbers mean? Herd immunity is the situation when so many people in the "herd" are immune to the virus, that the virus can't find enough people to infect, and dies out. Historically, this has been the only way that epidemics can end.

There are two ways to be immune to the virus. The first way is to become infected. My immune system sees the invader, and does the necessary things to kill it. And it remembers via mechanisms that we've evolved, so that the next time it sees the same (or similar) virus, it can go straight into action and kill it before it affects the body. The other way is to "teach" the body about this new virus - that is called vaccination, or immunisation. There is a third way, of course, and this is to die, but none of us want that.

So what percentage of people need to be immune, to reach herd immunity? The calculation is really quite simple.

Let's call the average number of people who get infected from one infected person, R0. If R0 is less than 1 then the virus will die out, and the nearer it is to zero, the faster it will die out.

If R0 is exactly 1, then each person infects one other person, if it is slightly less than 1, the virus slowly dies out.

What affects R0? A number of factors, such as  how the virus spreads, and how many virus particles does it take for it to take root. So for example, if it spreads through the air, it will be more infectious than if it can only spread by shaking hands. We measure the R0 by observation, you can't calculate it from the virus genome.

So, consider a virus with an R0 of 2. Each person infects two other people. But if one of those two is immune, then that drops the number infected to 1, and the virus can't grow. So, clearly, herd immunity for that virus would be 50%.

If a virus has an R0 of 10 (measles is 15) then nine out of those ten would need to be immune, so herd immunity happens at 90%, and that's why public health people are so keen on measles vaccinations for everyone.

And since Covid-19 (the disease that you get if infected by SARS-CoV-2) has an R0 of 3, so herd immunity happens when 2 out of 3 are immune. Herd immunity happens at 66%.

More generally, we can use the formula 

Herd immunity percentage = 100 - 100/R0

So what happens when everyone wears a mask? Masking interferes with the transmission of airborne viruses. It works in two ways. First, if someone is infected, then a mask will trap most of the virus particles they are shedding, because it will trap the droplets that they are carried on (especially coughs and sneezes, but also ordinary breathing). Second, if someone is not infected, then the mask will reduce the number of virus particles that they breathe in, and so reduce the likelihood of the virus being able to establish itself in a new victim.

So, suppose that masking reduces virus spreading by half, and the R0 falls from 3 to 1.5. We can put that number into the formula, and we find that we reach herd immunity at 33%.

But it isn't going to be possible to persuade every susceptible person to mask, or even every infected person to mask, because often people don't know that they are infected. So, masking will reduce the spread of the virus, and the population reaches herd immunity at a lower level of immunity. Not-masking means that you don't get to herd immunity until a lot more people are infected.

Vaccination isn't going to be perfect either. Flu vaccines are never 100% effective, and the Covid-19 vaccines won't be either. But a bigger problem (in some countries) will be vaccine refusal. And the people who refuse vaccines might be the same ones that refuse to mask. Countries that have such people will, of course, suffer far more than people who take the sensible precautions of masking and vaccination, but what can be done about that?

The campaign against cigarette smoking was massively successful; UK men smokers fell from 82% in 1948 to 14% today. Why was that? People were told the facts, and shown the consequences of smoking. We need to do the same for vaccination and masking. Show the facts and show the consequences.

Wednesday, 30 September 2020

Day 198 of self-isolation - Pugh, Pugh, Barney McGrew, Cuthbert, Dibble, Grubb

Pugh, Pugh, Barney McGrew, Cuthbert, Dibble, Grubb

71 deaths and 7143 new cases. It's rising horribly fast. 7143 is the worst number we've ever had. There's a lag between new cases and deaths of 2-3 weeks, and the number of new cases we had then was about 3000. So this is going to get a lot worse before it gets better.

Spain and France are also seeing disappointing numbers.

And the rules are so complicated that even our oven-ready Boris can't get them right. Does it have to be so complicated that people can't understand what they're supposed to do?

I accept that we're in a difficult situation, and we can't do a simple "lock down for everyone" like we did last spring. But how about this.

Set up seven different sets of rules, and make them as simple as possible, These different sets of rules would be for the various situations that can apply in various regions of the country.

So you have defcon 1 (no restrictions) up to defcon 7 (total lockdown). Defcon 2 to 6 would have various restrictions, carefully spelled out on the government web site.

Then you would simply announce "Camberwick Green is now at defcon 3, but will move to defcon 5 from Friday." And there would be an app, and a map on the government web site, that showed the defcon levels for each area. So, if Boris visits Camberwick Green, before he goes he checks out the defcon level, and when he's asked, he can answer using the defcon number, and if anyone wants them explained, he refers them to the government web site.



Tuesday, 29 September 2020

Day 197 of self-isolation - the second wave in Israel

The second wave in Israel

Israel did very well in the first wave of Covid, experiencing less than 10 deaths per day at the peak, and 600 new cases per day.

Not so good in the second wave. The seven day moving average of deaths per day now is 30 with new infections per day at 6000.

So the deaths per infection in the first wave was 1.7%, and in the second wave 0.5%. This is the same thing we've been seeing elsewhere; the second wave is a lot less deadly than the first, because we've learned treatments that ameliorate the disease.

Monday, 28 September 2020

Day 196 of self-isolation - a million deaths

A million deaths

Today, the total dead from Covid-19 reached a million; this is six months into the pandemic.  Seasonal flu kills 300,000 to 650,000 each year.

The flu season starts soon - ladysolly and I are getting our flu jabs next week, because we would rather not be one of the 300,000 to 650,000.

But there isn't a vaccine for Covid-19 - yet. I'm still hopeful that the Oxford University vaccine will be available soon, and I'm hoping to be in the second wave of vaccinations (the first wave will be healthcare workers and others in the front line).

But what you really don't want, is to get both at once; that will double the awfulness.


Sunday, 27 September 2020

Day 195 of self-isolation - Florida, app, resistance

 Florida, app, resistance

Florida, where there are still more than 100 Covid deaths per day and around 3000 new cases per day, has decided to reopen bars and restaurants. Why?

Florida needs your money. If you spend a week in Florida, they get your money, and the infection that you picked up there, won't manifest until you've gone home, and it becomes someone else's problem.

The UK app

A third of tests can't be linked to the app. Our oven-ready government can't IT it's way out of a paper bag.

But only 18.2% of those who developed symptoms in the last week actually reported self-isolating.So maybe it doesn't matter that the tracking app is so poor.


Some thousands of people protested in Trafalgar Square against the measures to control the virus. One popular speaker was David Icke, the guy who claims that the Royal Family are lizards (he has many other fantasies).

Saturday, 26 September 2020

Day 194 of self-isolation - Dogs


Dogs have very sensitive noses. I was once part of an experiment to see if dogs could sniff cancer. I was one of the non-cancer subjects. I don't know what the outcome was.

But I do know that dogs are used to sniff out drugs at airports, and also money. There's some very heart-warming videos on Youtube - when the dog finds a stash, it's rewarded with a game of "fetch".

Now dogs are being used to sniff out Covid-19. The test takes just a few seconds and, according to the report, is nearly 100% accurate. You wipe your neck with a cloth, put it in a can and the dogs sniff it. There are four dogs in Helsinki airport sniffing at passengers. If the dog says you're positive, you're then invited to take a standard nasal swab test. The dogs are called ET, Kossi, Miina and Valo.

Dogs are faster and cheaper than laboratories, and they don't get infected.


Kossi the Covid sniffer dog

Friday, 25 September 2020

Day 193 of self-isolation - Test and trace

Test and trace

Hurrah! The world-beating "NHS Covid-19" app is now available. So as a keen supporter of the fight against Covid-19, I rushed to install it.

It needs IOS 13.5 or above.

I run an iPhone 6 plus, using IOS 12.4.8. I tried to update it, but Apple says I'm already up to date. I suspect that the problem is, my iPhone can't run IOS 13.5 because it isn't an iPhone 6S or above. I'm one iPhone version too short.

I don't know how common this problem is, but if an anti-Covid enthusiast like me can't run the NHS app, that doesn't bode well.

It's great that they translated it into ten languages, with more to follow. And I understand why you can't run it on an oldish iPhone 6 plus. But it would be good if they mentioned that on the NHS web site (and presumably there's a similar problem for Androids).

After diving deep into the web site, I discovered that it needs Android Marshmallow (v6.0), or IOS 13.5 or above.It also needs Bluetooth Low Energy (BLE) 4 or above.

The Scotland app needs IOS 13.0 or above, which wouldn't work for me either, but I wonder how they were able to do better than the world-beating NHS England app?

New models of Huawei smartphones launched from May 2019 will not be able to use the app, as the app uses Exposure Notifications. 

There's a list of phones that will work here.